sudo: required
language: python
jdk: openjdk8
services:
  - docker
python:
  - '3.6'
cache: pip
matrix:
  fast_finish: true

install:
  # Install Nextflow
  - mkdir /tmp/nextflow && cd /tmp/nextflow
  - wget -qO- get.nextflow.io | bash
  - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
  - mkdir -p ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests

env:
  - NXF_VER='18.10.1' SCRATCH='~' # Specify a minimum NF version that should be tested and work. Set SCRATCH for prince.config.
  - NXF_VER='' SCRATCH='~'        # Plus: get the latest NF version and check, that it works. Set SCRATCH for prince.config.

script:
  # Run the pipeline with the test profile and test remote config
  - |
      grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \
      tr -s ' ' | \
      cut -d " " -f 2 | \
      grep -v "czbiohub_aws" | \
      xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf --custom_config_base=${TRAVIS_BUILD_DIR} -profile {}